Re: [gmx-users] g_rdf and number of atoms to include

[Mark Abraham]

Enemark Soeren wrote:

Ahh, now I understand - sorry, Omer!

 

In fact, I have compared all three single hydrogen RDFs and they are 
identical and also relatively smooth. Since, however, with 3 times more 
data points (all three hydrogen atoms taken together) I get a different 
RDF, would that indicate that I do not have enough data after all?


Does your own data converge with itself as you go from half to 3/4 to 
all of the data? That's a necessary (but not sufficient) criterion.


Are RDFs known to be slow to converge? I have about 1000 water molecules 
and about 50+ glycine molecules, simulated for 10ns with 1ps sampling 
intervals. That should give me 500,000,000 data points for the 
distribution, right? Can I compare this number with the literature in 
which RDFs for, say, water-water interactions are reported?


How many data points at what interval do they have?

Mark

One important point, which was not really clear to me before was if, 
provided that I have enough data, the RDFs should be identical no matter 
whether I use 1, 2, or 3 hydrogen atoms for generating the RDF. As far 
as I understood, both yours and Omer’s responses indicate that the RDFs 
should be identical. Did I get that correctly?


 


Best regards,

Soren

 

 

 

 

*From:* gmx-users-boun...@gromacs.org 
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Dallas B. Warren

*Sent:* Thursday, October 22, 2009 6:56 AM
*To:* Discussion list for GROMACS users
*Subject:* RE: [gmx-users] g_rdf and number of atoms to include

 

Omar’s response answered that question on why they are different.  In 
the first one you are grouping all three into one group, second is just 
one of the hydrogen types.  The fact that the rdf you get is different 
indicates that all three hydrogens are not identical.  Have you compared 
the rdf for each hydrogen type individually?  Another factor may also be 
that in the first you have three times the number of data points, which 
can smooth out the curves more.


 


Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble 
a nail.


 

*From:* gmx-users-boun...@gromacs.org 
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Enemark Soeren

*Sent:* Wednesday, 21 October 2009 8:28 PM
*To:* Discussion list for GROMACS users
*Subject:* RE: [gmx-users] g_rdf and number of atoms to include

 


Hi Omer,

Thanks for your input.

 


Let me reformulate my problem:

 


I have glycine molecules in the form of zwitterions:

 


 ….

1ZGLY N1   0.560   0.337   0.388 -0.0759 -0.2488 -0.5471

1ZGLYH12   0.625   0.312   0.461  0.6035  0.5922 -0.4315

1ZGLYH23   0.601   0.311   0.299  0.1500 -0.3357 -1.5372

1ZGLYH34   0.553   0.433   0.388  0.5086  2.8817 -1.8023

1ZGLYCA5   0.426   0.272   0.403  0.3095  0.1790 -0.0455

1ZGLY   HA16   0.352   0.335   0.345 -0.9032  0.4782  0.1366

1ZGLY   HA27   0.433   0.173   0.358  0.7875  0.5369 -3.0389

1ZGLY C8   0.378   0.267   0.551  0.1816 -0.4672  0.1868

1ZGLY   OC19   0.449   0.218   0.644 -0.2820 -0.4080  0.2048

1ZGLY   OC2   10   0.263   0.320   0.559 -0.0662 -0.2935 -0.8010

 ….

 

Now, I am interested in the interaction between the amine group hydrogen 
atoms (H1, H2, and H3) and the water oxygen atom. Thus, I define 2 group 
in an index file:


1.   aH1H2H3 (which contains all H1, H2, and H3 atoms in the glycine 
molecules in my system)


2.   aOwat (which contains all oxygen atoms in the water molecules 
in my system)


 


However, I also tried setting up a different index file with the groups:

1.   aH1 (which contains all H1 atoms in my system)

2.   aOwat (like before)

 


I find that these 2 index files do not produce the same RDFs. Why is that?

 

 


Best regards,

Soren

 

*From:* gmx-users-boun...@gromacs.org 
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Omer Markovitch

*Sent:* Wednesday, October 21, 2009 4:27 PM
*To:* Discussion list for GROMACS users
*Subject:* Re: [gmx-users] g_rdf and number of atoms to include

 

On Wed, Oct 21, 2009 at 07:28, Enemark Soeren > wrote:


Dear users,

I would like to compare interactions between molecules by using RDF. I 
have tried looking at glycine and water, and compare the following two 
interactions:


1)  between the amine hydrogen atoms in glycine and the oxygen atom 
in water


2)  between the carboxyl oxygen atoms in glycine and the oxygen atom 
in water


However, my result in 1) depends on how many of the 3 hydrogen atoms I 
include in the calculations. Why is that?


If you mean that when focusing your RDF calculations on either one of 
the three hydrogens results in three different RDFs 

RE: [gmx-users] g_rdf and number of atoms to include

[Enemark Soeren]

Ahh, now I understand - sorry, Omer!

 

In fact, I have compared all three single hydrogen RDFs and they are
identical and also relatively smooth. Since, however, with 3 times more
data points (all three hydrogen atoms taken together) I get a different
RDF, would that indicate that I do not have enough data after all? 

 

Are RDFs known to be slow to converge? I have about 1000 water molecules
and about 50+ glycine molecules, simulated for 10ns with 1ps sampling
intervals. That should give me 500,000,000 data points for the
distribution, right? Can I compare this number with the literature in
which RDFs for, say, water-water interactions are reported?

 

One important point, which was not really clear to me before was if,
provided that I have enough data, the RDFs should be identical no matter
whether I use 1, 2, or 3 hydrogen atoms for generating the RDF. As far
as I understood, both yours and Omer's responses indicate that the RDFs
should be identical. Did I get that correctly?

 

Best regards,

Soren

 

 

 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Dallas B. Warren
Sent: Thursday, October 22, 2009 6:56 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] g_rdf and number of atoms to include

 

Omar's response answered that question on why they are different.  In
the first one you are grouping all three into one group, second is just
one of the hydrogen types.  The fact that the rdf you get is different
indicates that all three hydrogens are not identical.  Have you compared
the rdf for each hydrogen type individually?  Another factor may also be
that in the first you have three times the number of data points, which
can smooth out the curves more.

 

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology 
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Enemark Soeren
Sent: Wednesday, 21 October 2009 8:28 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] g_rdf and number of atoms to include

 

Hi Omer,

Thanks for your input.

 

Let me reformulate my problem:

 

I have glycine molecules in the form of zwitterions:

 

 

1ZGLY N1   0.560   0.337   0.388 -0.0759 -0.2488 -0.5471

1ZGLYH12   0.625   0.312   0.461  0.6035  0.5922 -0.4315

1ZGLYH23   0.601   0.311   0.299  0.1500 -0.3357 -1.5372

1ZGLYH34   0.553   0.433   0.388  0.5086  2.8817 -1.8023

1ZGLYCA5   0.426   0.272   0.403  0.3095  0.1790 -0.0455

1ZGLY   HA16   0.352   0.335   0.345 -0.9032  0.4782  0.1366

1ZGLY   HA27   0.433   0.173   0.358  0.7875  0.5369 -3.0389

1ZGLY C8   0.378   0.267   0.551  0.1816 -0.4672  0.1868

1ZGLY   OC19   0.449   0.218   0.644 -0.2820 -0.4080  0.2048

1ZGLY   OC2   10   0.263   0.320   0.559 -0.0662 -0.2935 -0.8010

 

 

Now, I am interested in the interaction between the amine group hydrogen
atoms (H1, H2, and H3) and the water oxygen atom. Thus, I define 2 group
in an index file:

1.   aH1H2H3 (which contains all H1, H2, and H3 atoms in the glycine
molecules in my system)

2.   aOwat (which contains all oxygen atoms in the water molecules
in my system)

 

However, I also tried setting up a different index file with the groups:

1.   aH1 (which contains all H1 atoms in my system)

2.   aOwat (like before)

 

I find that these 2 index files do not produce the same RDFs. Why is
that?

 

 

Best regards,

Soren

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Omer Markovitch
Sent: Wednesday, October 21, 2009 4:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_rdf and number of atoms to include

 

On Wed, Oct 21, 2009 at 07:28, Enemark Soeren  wrote:

Dear users,

I would like to compare interactions between molecules by using RDF. I
have tried looking at glycine and water, and compare the following two
interactions:

1)  between the amine hydrogen atoms in glycine and the oxygen atom
in water

2)  between the carboxyl oxygen atoms in glycine and the oxygen atom
in water 

However, my result in 1) depends on how many of the 3 hydrogen atoms I
include in the calculations. Why is that?

If you mean that when focusing your RDF calculations on either one of
the three hydrogens results in three different RDFs then it means that
each hydrogen feels water differently. I bet this difference is only for
the first peak of g(r) and the other peaks overlap between the three
RDFs. As for how reasonable this result, its not unlikely because
glycine has atleast 2 different types of hydrogens (say, C-H vs. N-H),
depending on the protona

[gmx-users] Setting up an infinitely hard wall

[Amit Choubey]

Hi everyone,
I have been trying to set up an "infinitely" hard potential wall.

I tried to use the available wall options and could not really get it to do
what i needed. I wanted a steep repulsive potential but when i created that,
the system was blowing up, reason being that it requires smaller time step
and i cant afford to have smaller time step.

My idea to overcome this issue is to just reverse the velocity of the
particle whenever it hits the wall. I am not sure if there is any thing in
GROMACS which does this but any suggestions will be very helpful.

If there is nothing set up for something like above, i would like to play
around with the code to figure it out. If this is the case, could somebody
direct me to a starting point.

Thank you
Amit
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RE: [gmx-users] g_rdf and number of atoms to include

[Dallas B. Warren]

Omar's response answered that question on why they are different.  In
the first one you are grouping all three into one group, second is just
one of the hydrogen types.  The fact that the rdf you get is different
indicates that all three hydrogens are not identical.  Have you compared
the rdf for each hydrogen type individually?  Another factor may also be
that in the first you have three times the number of data points, which
can smooth out the curves more.

 

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology 
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Enemark Soeren
Sent: Wednesday, 21 October 2009 8:28 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] g_rdf and number of atoms to include

 

Hi Omer,

Thanks for your input.

 

Let me reformulate my problem:

 

I have glycine molecules in the form of zwitterions:

 

 

1ZGLY N1   0.560   0.337   0.388 -0.0759 -0.2488 -0.5471

1ZGLYH12   0.625   0.312   0.461  0.6035  0.5922 -0.4315

1ZGLYH23   0.601   0.311   0.299  0.1500 -0.3357 -1.5372

1ZGLYH34   0.553   0.433   0.388  0.5086  2.8817 -1.8023

1ZGLYCA5   0.426   0.272   0.403  0.3095  0.1790 -0.0455

1ZGLY   HA16   0.352   0.335   0.345 -0.9032  0.4782  0.1366

1ZGLY   HA27   0.433   0.173   0.358  0.7875  0.5369 -3.0389

1ZGLY C8   0.378   0.267   0.551  0.1816 -0.4672  0.1868

1ZGLY   OC19   0.449   0.218   0.644 -0.2820 -0.4080  0.2048

1ZGLY   OC2   10   0.263   0.320   0.559 -0.0662 -0.2935 -0.8010

 

 

Now, I am interested in the interaction between the amine group hydrogen
atoms (H1, H2, and H3) and the water oxygen atom. Thus, I define 2 group
in an index file:

1.   aH1H2H3 (which contains all H1, H2, and H3 atoms in the glycine
molecules in my system)

2.   aOwat (which contains all oxygen atoms in the water molecules
in my system)

 

However, I also tried setting up a different index file with the groups:

1.   aH1 (which contains all H1 atoms in my system)

2.   aOwat (like before)

 

I find that these 2 index files do not produce the same RDFs. Why is
that?

 

 

Best regards,

Soren

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Omer Markovitch
Sent: Wednesday, October 21, 2009 4:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_rdf and number of atoms to include

 

On Wed, Oct 21, 2009 at 07:28, Enemark Soeren  wrote:

Dear users,

I would like to compare interactions between molecules by using RDF. I
have tried looking at glycine and water, and compare the following two
interactions:

1)  between the amine hydrogen atoms in glycine and the oxygen atom
in water

2)  between the carboxyl oxygen atoms in glycine and the oxygen atom
in water 

However, my result in 1) depends on how many of the 3 hydrogen atoms I
include in the calculations. Why is that?

If you mean that when focusing your RDF calculations on either one of
the three hydrogens results in three different RDFs then it means that
each hydrogen feels water differently. I bet this difference is only for
the first peak of g(r) and the other peaks overlap between the three
RDFs. As for how reasonable this result, its not unlikely because
glycine has atleast 2 different types of hydrogens (say, C-H vs. N-H),
depending on the protonation state. You might want to provide more
details on the system you are studying to get better answer.
I am assuming that the RDFs are converged so that including more
trajectory data and/or sampled molecules and/or changing bin size does
not result in a drastic change to the curves.

 

Does that mean that I cannot directly compare the strengths (RDF
peak height) of the two interactions as they are not based on the same
number of atoms? Does it also mean that I must always calculate RDFs by
using 1 atom on each of the particles/groups that I am comparing?

I am not sure how good it is to use the first peak of g(r) to analyze
strengths, but you should also consider the width and area under peak.
This peak is an average on all nearest neighbours, bonded or not, so it
might not give you a good estimate of the hydrogen bond, for example.
If you are unsure of your g(r) calc it just for water (that is - only
oxygen-oxygen of water-water). At long distances (~10 Angstroms) it
should fluctuate around 1.

Bests, Omer Markovitch. 

 

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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Mark Abraham]

Baofu Qiao wrote:

HI all,

I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD 
website. But both of them can only deal with single chain system. Take 
an example, if there are 10 proteins (+water) in my system,  how to 
convert to topology of the total system to .psf file? I tried to append 
the .psf. But VMD doesn't recognize the appended .psf file.


Find out how to generate a .psf using CHARMM/NAMD tools, then.

Mark
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Re: [gmx-users] how to mimick explicit hydrogen bonding

[Mark Abraham]

ms wrote:

Hi Mark,

Thanks for your answer.

Mark Abraham ha scritto:

There's nothing directional about the physics of a hydrogen bond, unless
your model makes it so. There'd be nothing intrinsically valid or
invalid with that either, so long as you parameterized the force field
under that assumption. If using rigid water models and/or other atomic
constraints where H-bonded atoms can't have a geometric distortion, I
suppose such a model might be necessary. It's still far from clear that
H-bonding is sufficiently different from other electrostatic
interactions to warrant special treatment (and thus reparameterization
of charges).


Ok, the problem is that I want to re-implement a quite minimal
coarse-grained FF (so no explicit solvent etc.) and a directional
interaction would be useful.


Well you should consider alternative software, then.


Can anyone give me hints on how to describe a directional
hydrogen-bond-like interaction?

You would not achieve this in GROMACS without code modification. A
special non-bonded list for H-bonded water (and maybe H-bonded
non-water) that didn't call the standard water inner loops would be
required.


I see. I asked because I think I've read that there were force fields
with explicit hydrogen bond treatment (some CHARMM?) that were imported
into Gromacs, and I thought there was some clever hack to get it working
-but I guess that it is not the case.


IIRC, CHARMM did have explicit H-bond models ages ago, but (again IIRC) 
they're not in the modern versions and not in the upcoming GROMACS port.


Mark
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Re: [gmx-users] why the force is so large in energy minimization

[Mark Abraham]

青 叶 wrote:
I did a energy minimization on a system contain one [AuCl4]- and 503 
water moleculars, by using a self-define non-bond interaction (which is 
obtain from ab-initio calculation), my em.mdp file is as follow:

title  = yqq
cpp= /usr/bin/cpp ; the c pre-processor
define = -DFLEXILBE
constraints= none
integrator = steep
energygrps  = AU CL OW H
energygrp_table   = AU OW AU H CL OW CL H
dt =0.002; ps!
nsteps =4
nstlist=10
ns_type=grid
rlist  =0.9
coulombtype=User
rcoulomb   =0.9
vdwtype=User
rvdw   =1.0
fourierspacing =0.12
fourier_nx =0
fourier_ny =0
fourier_nz =0
pme_order  =4
ewald_rtol =1e-5
optimize_fft   =yes
;
; Energy minimizing stuff
;
emtol  =500.0
emstep =0.005
 
and meanwhile, I have modifide the ffG43a1.rtp, ffG43a1bon.itp, 
ffG43a1nb.itp files in order to include the relative parameters. Then 
add a table.xvg (actually the default 6-12 Lennard Jones potential form, 
I just renamed it so it will be read for describing the interaction of 
atom pairs which are not list in the  energygrp_table section) and four 
table.xvg contain the interaction information of AU OW, AU CL, CL 
OW, CL H.

but unfortunatly, the corresponding em.log file is follow:
 
 
Stepsize too small, or no change in energy.

Converged to machine precision,
but not to the requested precision Fmax < 500
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
Steepest Descents converged to machine precision in 12 steps,
but did not reach the requested Fmax < 500.
Potential Energy  = -3.5686449e+04
Maximum force =  1.3609032e+04 on atom 1236
Norm of force =  1.6019813e+03
 M E G A - F L O P S   A C C O U N T I N G
   RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
   T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
   NF=No Forces
 Computing: M-Number M-Flops  % Flops
---
 VdW(T) 1.011752  54.63516.6
 Coul(T) + VdW(T)   2.659114 180.82055.0
 Outer nonbonded loop   0.261041   2.610 0.8
 NS-Pairs   4.096803  86.03326.2
 Reset In Box   0.012096   0.036 0.0
 Shift-X0.018168   0.109 0.0
 CG-CoM 0.018168   0.055 0.0
 Bonds  0.48   0.003 0.0
 Angles 0.72   0.012 0.0
 Impropers  0.24   0.005 0.0
 Virial 0.018708   0.337 0.1
 Settle 0.012072   3.899 1.2
---
 Total   328.553   100.0
---

 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
 Computing: Nodes Number G-CyclesSeconds %
---
 Neighbor search1 120.8440.877.7
 Force  1 120.1800.216.5
 Constraints1 230.0040.0 0.4
 Rest   1   0.0590.1 5.4
---
 Total  1   1.0861.0   100.0
---
   NODE (s)   Real (s)  (%)
   Time:  1.000  1.000100.0
   (Mnbf/s)   (MFlops)   (steps/hour)
Performance:  3.671328.55343200.0
Finished mdrun on node 0 Wed Oct 21 23:38:48 2009
 
the force is very large and I have tried to adjust "emstep" and other 
options but seems has no influence on the result, can anyone help me on 
this problem, any suggestion will be very, very grateful. Thank you.
By the way, I have ajusted the No. of water moleculars in the simulation 
box but almost has no infulence on the result.


The magnitude of the PE is such that you've probably not made any 
catastrophic errors. Make sure you get the sign of the table columns 
correct for various derivatives correct. Otherwise, have a look at atom 
1236 and see what might be wrong in that region.


Mark
__

Re: [gmx-users] COM removal type angular with PBC?

[Mark Abraham]

jennifer johnston wrote:

Dear All,
I'm attempting to simulate a dimeric protein in an explicit 
bilayer/water environment. I'd like to remove the translation & rotation 
of one protomer relative to the other, so that one protomer is able to 
move around relative to the stationary one. I'm using semiisotropic 
pressure coupling.


That's not yet a well-formed strategy. What motions are to be permitted 
relative to the bilayer?


I looked at using COMM_MODE = angular, with the comm group being the 
backbone of the stationary protomer. (This is because I'd prefer not to 
apply posres to individual backbone atoms, if possible...)
I ran the simulation, adn it seems that the stationary protomer is not 
really anymore stationary than the free one.
When I look at the posts relating to the use of angular com motion 
removal, most of the discussion seems to suggest that it is not 
advisable to use angular com motion removal with PBC, and not really 
advisable to use it for a small part of a system, as I've tried to do.. 
but much of the discussion relates to vacuum simulations. Do I conclude 
correctly, that what I've tried just categorically will not work for an 
explicit system??


Finally - if I am correct - then is there a different way of applying a 
position restraint to the com of a group - rather than to explicit atoms?


No there's no implementation of that.

Mark
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Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

[Mark Abraham]

ram bio wrote:

Dear Justin,

Thanks for the suggestion and advice.
As i have used a modelled protein and want to obtain the lowest energy
configuration of the protein by doing dynamics, 


That's all very well, but what will that give you other than a set where 
the partition of total energy into potential and kinetic was skewed one way?


Mark
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[gmx-users] COM removal type angular with PBC?

[jennifer johnston]

Dear All,
I'm attempting to simulate a dimeric protein in an explicit bilayer/water environment. I'd like to remove the translation & rotation of one protomer relative to the other, so that one protomer is able to move around relative to the stationary one. I'm using semiisotropic pressure coupling.
I looked at using COMM_MODE = angular, with the comm group being the backbone of the stationary protomer. (This is because I'd prefer not to apply posres to individual backbone atoms, if possible...)
I ran the simulation, adn it seems that the stationary protomer is not really anymore stationary than the free one.
When I look at the posts relating to the use of angular com motion removal, most of the discussion seems to suggest that it is not advisable to use angular com motion removal with PBC, and not really advisable to use it for a small part of a system, as I've tried to do.. but much of the discussion relates to vacuum simulations. Do I conclude correctly, that what I've tried just categorically will not work for an explicit system?? 

Finally - if I am correct - then is there a different way of applying a position restraint to the com of a group - rather than to explicit atoms?
Many thanks in advance for your help,
Jennifer
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Re: [gmx-users] Extended trajectory

[Arik Cohen]

Thanks allot for all your help

Arik

Justin A. Lemkul wrote:



Arik Cohen wrote:

Hi,

I'll be most thankful if someone could tell me how to run a 
fragmented trajectory using only the mdrun command. As of now I'm 
using :


while(SimuTime < SimTime)
   {
  ...
system("tpbconv -s run.tpr -f run.trr -e run.edr -extend 1.0 -o 
run.tpr");
system("mdrun -cpi run.cpt -cpo run.cpt -append -npme 0 -v 
-deffnm run");


   }

When I ran the above mdrun command alone, the run got stack



No error message?  Just stuck?  It could be that you're trying to read 
and write to the same file names.  I think your method of preparing 
the extended run is also malformed, since the advent of checkpoint 
files.  See here:


http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

Try with the syntax and naming convention given there (to avoid 
potential I/O confusion) and see if your run works.


-Justin


Thanks

Arik
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Re: [gmx-users] Extended trajectory

[Justin A. Lemkul]

Arik Cohen wrote:

Hi,

I'll be most thankful if someone could tell me how to run a fragmented 
trajectory using only the mdrun command. As of now I'm using :


while(SimuTime < SimTime)
   {
  ...
system("tpbconv -s run.tpr -f run.trr -e run.edr -extend 1.0 -o 
run.tpr");
system("mdrun -cpi run.cpt -cpo run.cpt -append -npme 0 -v -deffnm 
run");


   }

When I ran the above mdrun command alone, the run got stack



No error message?  Just stuck?  It could be that you're trying to read and write 
to the same file names.  I think your method of preparing the extended run is 
also malformed, since the advent of checkpoint files.  See here:


http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

Try with the syntax and naming convention given there (to avoid potential I/O 
confusion) and see if your run works.


-Justin


Thanks

Arik
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Extended trajectory

[Arik Cohen]

Hi,

I'll be most thankful if someone could tell me how to run a fragmented 
trajectory using only the mdrun command. As of now I'm using :


while(SimuTime < SimTime)
   {
  ...
system("tpbconv -s run.tpr -f run.trr -e run.edr -extend 1.0 -o 
run.tpr");
system("mdrun -cpi run.cpt -cpo run.cpt -append -npme 0 -v -deffnm 
run");


   }

When I ran the above mdrun command alone, the run got stack

Thanks

Arik
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[gmx-users] PMF and g_wham

[Stefan Hoorman]

While using g_wham to obtain a PMF from umbrella sampling simulations I came
up with the following problem. I have simulated my windows with a 0.1nm
difference between structures starting from the initial position where my
dimer is equilibrated and ending 0.5nm farther than what the lennard jones
and coulomb interactions between these structures exist. When I include all
these windows including the last 5 ones where my structures do not interact,
my profile.xvg comes out as a straight line at zero energy. The histogram
file looks fine, but the profile comes out wrong. When I do not include
these last 5 windows my profile comes out as expected but there seems to be
no final plateau. Is this normal in g_wham? Any advice on the matter would
be great.
Thank you
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[gmx-users] alternative means of calculating PMF

[chris . neale]

Hi Stefan,

If you know the bound state, you can use the double decoupling method  
to decouple the bound state and then recouple into bulk solvent.


Note that both decoupling and umbrella sampling methods will require  
that you make the appropriate corrections to standard state values and  
that this correction may be what you are missing with your umbrella  
sampling results.


I outline the way to get US standard state free energies, and this is  
a very quick description so please refer to peer reviewed papers for  
something that is more complete.


1. Boltzmann integrate your PMF (E_i values) over the bound state.

G_bound=-1/Bln*sum over i [exp(-BE_i)*delta_i]

2. Define your unbound energy (E_ub) from your PMF and Boltzmann  
integrate it over a distance, dist, such that the volume per monomer  
will be 1.66 nm^3 (volume per molecule at 1 M concentration).


G_unbound=-1/Bln[exp(-BE_ub)*dist]

3. dG_binding = G_bound - G_unbound

Where I have here neglected any corrections for constraints (i.e. I  
assumed that you reaction coordinate is a Center of Mass relation or  
something similar).


Also, note that the form of equation 2 assumes that you have already  
extracted the increasing volume portion of your PMF if you simply use  
the distance between centers of mass. Therefore if you have not done  
this then your equation 2 will be of a form like equation 1, except  
that you integrate over an unbound region for a total of 1.66 nm^3.


Finally, make sure that you take both monomers into account in your  
final calculations correctly so that your final concentration of  
unbound monomer is really 1 M, not 0.5 M or 2 M.


And if your monomers are so big that the bound state occupies a volume  
greater than 2*1.66 nm^3 just set your standard state to 0.1 M or  
something and then make a final correction back to 1 M later.


Good luck,
Chris.


--- original message ---

Hello.
I have finished calculating the PMF of dimerization for my system using
umbrella sampling and WHAM. But came up with some free energy values that
are not compatible to the ones found in other works. I have alread had
several instrutions and tips from Justin in past email here in gms users'
list, and since now I believe there are no more variables to change in my
calculations, I believe another method (implemented in gromacs) would help
me compare results and justify my findings.
I read something in the users'list about instead of using umbrella sampling
I would use constraints in order to separate my system's components. But I
was not able to find anything more specific about this type of calculation
on the manual.
Some help on the matter would be of great help
Thank you

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[gmx-users] alternative means of calculating PMF

[Stefan Hoorman]

Hello.
I have finished calculating the PMF of dimerization for my system using
umbrella sampling and WHAM. But came up with some free energy values that
are not compatible to the ones found in other works. I have alread had
several instrutions and tips from Justin in past email here in gms users'
list, and since now I believe there are no more variables to change in my
calculations, I believe another method (implemented in gromacs) would help
me compare results and justify my findings.
I read something in the users'list about instead of using umbrella sampling
I would use constraints in order to separate my system's components. But I
was not able to find anything more specific about this type of calculation
on the manual.
Some help on the matter would be of great help
Thank you
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[gmx-users] why the force is so large in energy minimization

[青 叶]

I did a energy minimization on a system contain one [AuCl4]- and 503 water 
moleculars, by using a self-define non-bond interaction (which is obtain from 
ab-initio calculation), my em.mdp file is as follow:
title  = yqq
cpp    = /usr/bin/cpp ; the c pre-processor
define = -DFLEXILBE
constraints    = none
integrator = steep
energygrps  = AU CL OW H
energygrp_table   = AU OW AU H CL OW CL H
dt =0.002; ps!
nsteps =4
nstlist    =10
ns_type    =grid
rlist  =0.9
coulombtype    =User
rcoulomb   =0.9
vdwtype    =User
rvdw   =1.0
fourierspacing =0.12
fourier_nx =0
fourier_ny =0
fourier_nz =0
pme_order  =4
ewald_rtol =1e-5
optimize_fft   =yes
;
; Energy minimizing stuff
;
emtol  =500.0
emstep =0.005
 
and meanwhile, I have modifide the ffG43a1.rtp, ffG43a1bon.itp, ffG43a1nb.itp 
files in order to include the relative parameters. Then add a table..xvg 
(actually the default 6-12 Lennard Jones potential form, I just renamed it so 
it will be read for describing the interaction of atom pairs which are not list 
in the  energygrp_table section) and four table.xvg contain the interaction 
information of AU OW, AU CL, CL OW, CL H.
but unfortunatly, the corresponding em.log file is follow:
 
 
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 500
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
Steepest Descents converged to machine precision in 12 steps,
but did not reach the requested Fmax < 500.
Potential Energy  = -3.5686449e+04
Maximum force =  1.3609032e+04 on atom 1236
Norm of force =  1.6019813e+03
 M E G A - F L O P S   A C C O U N T I N G
   RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
   T=Tabulated    W3=SPC/TIP3p    W4=TIP4p (single or pairs)
   NF=No Forces
 Computing: M-Number M-Flops  % Flops
---
 VdW(T) 1.011752  54.635    16.6
 Coul(T) + VdW(T)   2.659114 180.820    55.0
 Outer nonbonded loop   0.261041   2.610 0.8
 NS-Pairs   4.096803  86.033    26.2
 Reset In Box   0.012096   0.036 0.0
 Shift-X    0.018168   0.109 0.0
 CG-CoM 0.018168   0.055 0.0
 Bonds  0.48   0.003 0.0
 Angles 0.72   0.012 0.0
 Impropers  0.24   0.005 0.0
 Virial 0.018708   0.337 0.1
 Settle 0.012072   3.899 1.2
---
 Total   328.553   100.0
---

 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
 Computing: Nodes Number G-Cycles    Seconds %
---
 Neighbor search    1 12    0.844    0.8    77.7
 Force  1 12    0.180    0.2    16.5
 Constraints    1 23    0.004    0.0 0.4
 Rest   1   0.059    0.1 5.4
---
 Total  1   1.086    1.0   100.0
---
   NODE (s)   Real (s)  (%)
   Time:  1.000  1.000    100.0
   (Mnbf/s)   (MFlops)   (steps/hour)
Performance:  3.671    328.553    43200.0
Finished mdrun on node 0 Wed Oct 21 23:38:48 2009
 
the force is very large and I have tried to adjust "emstep" and other options 
but seems has no influence on the result, can anyone help me on this problem, 
any suggestion will be very, very grateful. Thank you.
By the way, I have ajusted the No. of water moleculars in the simulation box 
but almost has no infulence on the result.


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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Nicolas Sapay]

Hello everybody,

Here is the rtf file I mentioned previously. It can be used by PSFGEN to 
generate a psf file from pdb files. The result can be used, for example, 
by the PME Electrostatics plugin of VMD. PSFGEN is available as a VMD 
plugin or as an independant executable.


Nicolas

Nicolas SAPAY a écrit :

Hi,

All TCL scripts dowloaded from the VMD website as well as mine are
supposed to be used within VMD. You have to run VMD first, then source the
script. Alternatively, you can source it in your .vmdrc file. After that,
you can run the g_cg function

Nicolas

  




  
  


HI all,

I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD
website. But both of them can only deal with single chain system. Take
an example, if there are 10 proteins (+water) in my system,  how to
convert to topology of the total system to .psf file? I tried to append
the .psf. But VMD doesn't recognize the appended .psf file.

Another question: 
How to use the code from Nicolas? I got the following error information
from 
 ./coarse_grain.tcl -tpr em.tpr

: command not found line 10:
./coarse_grain.tcl: line 14: proc: command not found
: command not found line 15:
./coarse_grain.tcl: line 17: global: command not found
./coarse_grain.tcl: line 18: global: command not found
./coarse_grain.tcl: line 19: global: command not found
./coarse_grain.tcl: line 20: global: command not found
./coarse_grain.tcl: line 21: global: command not found
./coarse_grain.tcl: line 22: global: command not found
./coarse_grain.tcl: line 23: global: command not found
./coarse_grain.tcl: line 24: global: command not found
./coarse_grain.tcl: line 25: global: command not found
: command not found line 26:
: command not found line 41:
: command not found line 45:
./coarse_grain.tcl: line 120: syntax error near unexpected token `}'
'/coarse_grain.tcl: line 120: ` } else {

best wishes,
Baofu Qiao

Nicolas SAPAY wrote:

  
Justin A. Lemkul wrote:


  I have also added a Perl script to the GROMACS site
(the VMD page):

http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD";>http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD

The user provides an input topology file, and a .psf file is written,
which can be loaded as data for the structure in VMD.  The !NBOND
section seems to be the most important in this regard, so the other
sections are a bit rough, but it seems to work alright.

The caveat is the topology must be one generated by MARTINI, in order to
satisfy all the pattern matching and the order of the topology.  It
should be fairly easy to modify the program further to accommodate other
layouts, but I haven't had the need to do so.
  

I added text to the above page describing both scripts,
which are
attached. I'd have done that yesterday but the website was
intermittently down.

  
  
Thanks for posting the tcl script on the website, although this script has
been mainly coded by someone else. I have simply modified it for my own
purpose.

I also want to mention it is a good think to create a psf file if one work
with VMD. You store at once, bonds, atom types and charges. Actually, I
should have somewhere a .rtf file for the Martini amino acids and lipids
(the equivalent of the Gromacs rtp file for CHARMM). It can be used by
psfgen to generate a psf file with Martini bonds, charges and atom types.
If I can retrieve it in my archives, I will post it on the website.

Nicolas

  
  
Mark



  Nicolas Sapay wrote:
  
  
Hello Thomas,

I have a tcl script in my personal script library that might do what
you want to do. I didn't use it for quite a while, but it was working
well as far as I remember. I think it has been adapted from a script
available on the VMD website, but I don't remember exactly its
history. It doesn't seem too difficult to understand. You should be
able to modify it for your own purpose, if needed.

Cheers,
Nicolas


Thomas Schmidt a écrit :


  Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can
use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas


  

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Re: [gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

[Justin A. Lemkul]

Pablo Englebienne wrote:
OK, I started over with the CHCl3 box from scratch. I prepared the 
following itp file from the CHCL3 parameters in ffG53a5.rtp:


---[chcl3.itp]---
[ moleculetype ]
; Namenrexcl
CHCL3 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
1   HCHL  1  CHCL3   HChL  1  0.082  1.008   
2   CCHL  1  CHCL3   CChL  1  0.179 12.011  
3  CLCHL  1  CHCL3  CLCh1  1 -0.087 35.453 
4  CLCHL  1  CHCL3  CLCh2  1 -0.087 35.453 
5  CLCHL  1  CHCL3  CLCh3  1 -0.087 35.453


[ bonds ]
;  aiaj funct   1 2 2gb_39
   2 3 2gb_40
   2 4 2gb_40
   2 5 2gb_40
   1 3 2gb_47
   1 4 2gb_47
   1 5 2gb_47
   3 4 2gb_48
   3 5 2gb_48
   4 5 2gb_48

[ angles ]
;  aiajak funct 1 2 3 2  ga_43
   1 2 4 2  ga_43
   1 2 5 2  ga_43
   3 2 4 2  ga_44
   3 2 5 2  ga_44
   4 2 5 2  ga_44
---[chcl3.itp]---

I noticed that G53a5 includes 4 types of bond stretching terms specific 
for CHCl3 (C-Cl, C-H, H-Cl and Cl-Cl), therefore I specified all of 
them. Should all of these terms be harmonic bonds (function type 2) or 
some (e.g., the H-Cl and Cl-Cl terms) should be type 6 (as described in 
section 5.4 of the manual)? I tried with both types and I get the same 
minimized structure with the following topology and mdp files:




The bonds defined correspond with what I get when I run pdb2gmx on a chloroform 
molecule, so I would suspect you have them properly defined as function type 2, 
although pdb2gmx defines many more angles and even dihedrals, probably given the 
weird bonding setup in CHCl3.  I don't know how that might affect your system.


I also discovered a minor bug in the Gromos96 .rtp files in the CHCl3 directive 
- no bond is defined between C and H.  Will file a bugzilla.


-Justin


---[topol.top]---
; Include forcefield parameters
#include "ffG53a5.itp"
#include "chcl3.itp"

[ system ]
; Name
Chloroform

[ molecules ]
; Compound#mols
CHCL3 1
---[topol.top]---

---[em.mdp]---
integrator  =  cg
nsteps  =  5
;
;Energy minimizing stuff
;
emtol   =  1e-5
emstep  =  0.01

;
;Electrostatics
;
coulombtype =  cut-off
rcoulomb=  0
ns_type =  simple
nstlist =  0
rlist=  0

;
;vdW
;
rvdw=  0

;
;   PBC
;
pbc=  no
---[em.mdp]---

In the minimized structure, not all C-Cl distances are equivalent, 
although the minimization converges OK.


Any comments?

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

[ram bio]

Dear Justin,

Thanks for the advice, will try to follow using grace.

Ram

On Wed, Oct 21, 2009 at 8:25 PM, Justin A. Lemkul  wrote:
>
>
> ram bio wrote:
>>
>> Dear Justin.
>>
>> Thanks for the suggestion, definitely i would run next time for a
>> longer time 2-10 ns.
>> Here, I want to learn the analysis part of the mdrun, In order to
>> locate the lowest energy frame  I executed command g_energy -f
>> md_0_1.edr -o PE.xvg and the output was
>>
>> Statistics over 51 steps [ 0. thru 1000.0001 ps ], 1 data sets
>> All averages are exact over 51 steps
>>
>> Energy  Average   RMSD Fluct.  Drift
>>  Tot-Drift
>>
>> ---
>> Potential-1.2189e+061115.541070.01-1.0927
>>  -1092.7
>>
>> then I had a look at the PE.xvg file, but the values are very close to
>> identify the lowest energy point, i also tried to a have a look at the
>> md_0_1.log file, here also it is tedious and time consuming and the
>> values are close to remember. Can you suggest me how to locate the
>> lowest energy frame, so that i can use the comand (below) to retrieve
>> that particular frame coordinates in PDB file:
>>
>
> I would suggest writing a script.  I think plotting tools like Grace can
> also extract minimum values from data sets.  If the values are so close
> together, then ask yourself whether the lowest of these values is
> significantly different from any of the other conformation.  Also, an RMSD
> analysis will tell you how much the structure has changed (or is changing).
>
>> trjconv -f md_0_1.xtc -o LEconf.pdb -dump framenumber (any frame
>> number- corresponding to the lowest energy)
>>
>>
>> and also please tell the whether the command i am going to use to
>> retrieve the lowest energy configuration is correct.
>
> Close.  You also need to use -s when interconverting formats (I believe),
> and -dump is not given a frame number, but rather a time in ps.
>
>>
>> Thanks,
>>
>> Ram
>>
>>
>> On Wed, Oct 21, 2009 at 7:37 PM, Justin A. Lemkul  wrote:
>>>
>>> ram bio wrote:

 Dear Justin,

 Thanks for the suggestion and advice.
 As i have used a modelled protein and want to obtain the lowest energy
 configuration of the protein by doing dynamics, i want to collect the
 structure (coordinates in pdb) representing average of all the
 frames/configurations produced in MD and also the lowest energy
 configuration structure (coordinates in PDB) produced during the
 simulation, which can be used for docking. Please help how to obtain
 the average structure as well as the lowest energy configuration
 structure.

>>> Average structures are not always meaningful (or even
>>> physically-relevant):
>>>
>>> http://www.gromacs.org/Documentation/Terminology/Average_Structure
>>>
>>> You can get average structures from, i.e. g_cluster -cl, if you want.  As
>>> for the lowest energy structure, analyze potential energy, and dump out
>>> the
>>> frame corresponding to the lowest point.  Hopefully you saved coordinates
>>> and energies at the same interval :)  The potential energy will
>>> correspond
>>> to that of the system, but hopefully it should give some indication of
>>> the
>>> lowest energy configuration.  I don't know anything about your system,
>>> but
>>> it will also depend on how much the energy fluctuates as to how relevant
>>> this structure might be, and how different it might be from an "average."
>>>
>>> If your structure comes from some model you built, realize that 1 ns is
>>> an
>>> exceptionally short time frame, especially given the capabilities of
>>> modern
>>> hardware and the speed of the GROMACS code.  You may want to consider
>>> running a bit longer to ensure that you really have a stable system.
>>>
>>> -Justin
>>>
>>> --
>>> 
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> 
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface
>>> or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> ___

[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

[Pablo Englebienne]

OK, I started over with the CHCl3 box from scratch. I prepared the following 
itp file from the CHCL3 parameters in ffG53a5.rtp:

---[chcl3.itp]---
[ moleculetype ]
; Namenrexcl
CHCL3 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
1   HCHL  1  CHCL3   HChL  1  0.082  1.008   
2   CCHL  1  CHCL3   CChL  1  0.179 12.011  
3  CLCHL  1  CHCL3  CLCh1  1 -0.087 35.453 
4  CLCHL  1  CHCL3  CLCh2  1 -0.087 35.453 
5  CLCHL  1  CHCL3  CLCh3  1 -0.087 35.453


[ bonds ]
;  aiaj funct
   1 2 2gb_39

   2 3 2gb_40
   2 4 2gb_40
   2 5 2gb_40
   1 3 2gb_47
   1 4 2gb_47
   1 5 2gb_47
   3 4 2gb_48
   3 5 2gb_48
   4 5 2gb_48

[ angles ]
;  aiajak funct  
   1 2 3 2  ga_43

   1 2 4 2  ga_43
   1 2 5 2  ga_43
   3 2 4 2  ga_44
   3 2 5 2  ga_44
   4 2 5 2  ga_44
---[chcl3.itp]---

I noticed that G53a5 includes 4 types of bond stretching terms specific for 
CHCl3 (C-Cl, C-H, H-Cl and Cl-Cl), therefore I specified all of them. Should 
all of these terms be harmonic bonds (function type 2) or some (e.g., the H-Cl 
and Cl-Cl terms) should be type 6 (as described in section 5.4 of the manual)? 
I tried with both types and I get the same minimized structure with the 
following topology and mdp files:

---[topol.top]---
; Include forcefield parameters
#include "ffG53a5.itp"
#include "chcl3.itp"

[ system ]
; Name
Chloroform

[ molecules ]
; Compound#mols
CHCL3 1
---[topol.top]---

---[em.mdp]---
integrator  =  cg
nsteps  =  5
;
;   Energy minimizing stuff
;
emtol   =  1e-5
emstep  =  0.01

;
;   Electrostatics
;
coulombtype =  cut-off
rcoulomb=  0
ns_type =  simple
nstlist =  0
rlist   =  0

;
;   vdW
;
rvdw=  0

;
;   PBC
;
pbc =  no
---[em.mdp]---

In the minimized structure, not all C-Cl distances are equivalent, although the 
minimization converges OK.

Any comments?

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Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

[Justin A. Lemkul]

ram bio wrote:

Dear Justin.

Thanks for the suggestion, definitely i would run next time for a
longer time 2-10 ns.
Here, I want to learn the analysis part of the mdrun, In order to
locate the lowest energy frame  I executed command g_energy -f
md_0_1.edr -o PE.xvg and the output was

Statistics over 51 steps [ 0. thru 1000.0001 ps ], 1 data sets
All averages are exact over 51 steps

Energy  Average   RMSD Fluct.  Drift  Tot-Drift
---
Potential-1.2189e+061115.541070.01-1.0927-1092.7

then I had a look at the PE.xvg file, but the values are very close to
identify the lowest energy point, i also tried to a have a look at the
md_0_1.log file, here also it is tedious and time consuming and the
values are close to remember. Can you suggest me how to locate the
lowest energy frame, so that i can use the comand (below) to retrieve
that particular frame coordinates in PDB file:



I would suggest writing a script.  I think plotting tools like Grace can also 
extract minimum values from data sets.  If the values are so close together, 
then ask yourself whether the lowest of these values is significantly different 
from any of the other conformation.  Also, an RMSD analysis will tell you how 
much the structure has changed (or is changing).



trjconv -f md_0_1.xtc -o LEconf.pdb -dump framenumber (any frame
number- corresponding to the lowest energy)


and also please tell the whether the command i am going to use to
retrieve the lowest energy configuration is correct.


Close.  You also need to use -s when interconverting formats (I believe), and 
-dump is not given a frame number, but rather a time in ps.




Thanks,

Ram


On Wed, Oct 21, 2009 at 7:37 PM, Justin A. Lemkul  wrote:


ram bio wrote:

Dear Justin,

Thanks for the suggestion and advice.
As i have used a modelled protein and want to obtain the lowest energy
configuration of the protein by doing dynamics, i want to collect the
structure (coordinates in pdb) representing average of all the
frames/configurations produced in MD and also the lowest energy
configuration structure (coordinates in PDB) produced during the
simulation, which can be used for docking. Please help how to obtain
the average structure as well as the lowest energy configuration
structure.


Average structures are not always meaningful (or even physically-relevant):

http://www.gromacs.org/Documentation/Terminology/Average_Structure

You can get average structures from, i.e. g_cluster -cl, if you want.  As
for the lowest energy structure, analyze potential energy, and dump out the
frame corresponding to the lowest point.  Hopefully you saved coordinates
and energies at the same interval :)  The potential energy will correspond
to that of the system, but hopefully it should give some indication of the
lowest energy configuration.  I don't know anything about your system, but
it will also depend on how much the energy fluctuates as to how relevant
this structure might be, and how different it might be from an "average."

If your structure comes from some model you built, realize that 1 ns is an
exceptionally short time frame, especially given the capabilities of modern
hardware and the speed of the GROMACS code.  You may want to consider
running a bit longer to ensure that you really have a stable system.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


___
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

[ram bio]

Dear Justin.

Thanks for the suggestion, definitely i would run next time for a
longer time 2-10 ns.
Here, I want to learn the analysis part of the mdrun, In order to
locate the lowest energy frame  I executed command g_energy -f
md_0_1.edr -o PE.xvg and the output was

Statistics over 51 steps [ 0. thru 1000.0001 ps ], 1 data sets
All averages are exact over 51 steps

Energy  Average   RMSD Fluct.  Drift  Tot-Drift
---
Potential-1.2189e+061115.541070.01-1.0927-1092.7

then I had a look at the PE.xvg file, but the values are very close to
identify the lowest energy point, i also tried to a have a look at the
md_0_1.log file, here also it is tedious and time consuming and the
values are close to remember. Can you suggest me how to locate the
lowest energy frame, so that i can use the comand (below) to retrieve
that particular frame coordinates in PDB file:

trjconv -f md_0_1.xtc -o LEconf.pdb -dump framenumber (any frame
number- corresponding to the lowest energy)


and also please tell the whether the command i am going to use to
retrieve the lowest energy configuration is correct.

Thanks,

Ram


On Wed, Oct 21, 2009 at 7:37 PM, Justin A. Lemkul  wrote:
>
>
> ram bio wrote:
>>
>> Dear Justin,
>>
>> Thanks for the suggestion and advice.
>> As i have used a modelled protein and want to obtain the lowest energy
>> configuration of the protein by doing dynamics, i want to collect the
>> structure (coordinates in pdb) representing average of all the
>> frames/configurations produced in MD and also the lowest energy
>> configuration structure (coordinates in PDB) produced during the
>> simulation, which can be used for docking. Please help how to obtain
>> the average structure as well as the lowest energy configuration
>> structure.
>>
>
> Average structures are not always meaningful (or even physically-relevant):
>
> http://www.gromacs.org/Documentation/Terminology/Average_Structure
>
> You can get average structures from, i.e. g_cluster -cl, if you want.  As
> for the lowest energy structure, analyze potential energy, and dump out the
> frame corresponding to the lowest point.  Hopefully you saved coordinates
> and energies at the same interval :)  The potential energy will correspond
> to that of the system, but hopefully it should give some indication of the
> lowest energy configuration.  I don't know anything about your system, but
> it will also depend on how much the energy fluctuates as to how relevant
> this structure might be, and how different it might be from an "average."
>
> If your structure comes from some model you built, realize that 1 ns is an
> exceptionally short time frame, especially given the capabilities of modern
> hardware and the speed of the GROMACS code.  You may want to consider
> running a bit longer to ensure that you really have a stable system.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

[Justin A. Lemkul]

ram bio wrote:

Dear Justin,

Thanks for the suggestion and advice.
As i have used a modelled protein and want to obtain the lowest energy
configuration of the protein by doing dynamics, i want to collect the
structure (coordinates in pdb) representing average of all the
frames/configurations produced in MD and also the lowest energy
configuration structure (coordinates in PDB) produced during the
simulation, which can be used for docking. Please help how to obtain
the average structure as well as the lowest energy configuration
structure.



Average structures are not always meaningful (or even physically-relevant):

http://www.gromacs.org/Documentation/Terminology/Average_Structure

You can get average structures from, i.e. g_cluster -cl, if you want.  As for 
the lowest energy structure, analyze potential energy, and dump out the frame 
corresponding to the lowest point.  Hopefully you saved coordinates and energies 
at the same interval :)  The potential energy will correspond to that of the 
system, but hopefully it should give some indication of the lowest energy 
configuration.  I don't know anything about your system, but it will also depend 
on how much the energy fluctuates as to how relevant this structure might be, 
and how different it might be from an "average."


If your structure comes from some model you built, realize that 1 ns is an 
exceptionally short time frame, especially given the capabilities of modern 
hardware and the speed of the GROMACS code.  You may want to consider running a 
bit longer to ensure that you really have a stable system.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] scripts to generate topology CG

[sunny mishra]

There is a seq2itp.pl script provided by martini folks in their
website. You can get it from there.

Sunny

On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra
 wrote:
> Hi:
> I am looking for scripts that generate topology in coarse grained.
> Thanks for indications.
>
> francesco pietra
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[gmx-users] scripts to generate topology CG

[Francesco Pietra]

Hi:
I am looking for scripts that generate topology in coarse grained.
Thanks for indications.

francesco pietra
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Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

[ram bio]

Dear Justin,

Thanks for the suggestion and advice.
As i have used a modelled protein and want to obtain the lowest energy
configuration of the protein by doing dynamics, i want to collect the
structure (coordinates in pdb) representing average of all the
frames/configurations produced in MD and also the lowest energy
configuration structure (coordinates in PDB) produced during the
simulation, which can be used for docking. Please help how to obtain
the average structure as well as the lowest energy configuration
structure.

Thanks,

Ram

On Wed, Oct 21, 2009 at 6:08 PM, Justin A. Lemkul  wrote:
>
>
> ram bio wrote:
>>
>> Dear Mark,
>>
>> Thanks for the advice and suggestions.
>>
>> I have used trjconv command as in the justin tutorial (trjconv -s
>> md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact),
>> but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD,
>> i could not see the protein jumping out of the box on one side. I am
>> doing something wrong, Please let me know, and  was able to calculate
>> rmsd plot as per the command: g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc
>> -o rmsd.xvg -tu ns
>>
>
> If you don't see the protein jumping, then what's the problem?  That's the
> point of using trjconv - to correct periodicity.
>
>>
>> and i want convert the coordinates of the simulated protein in pdb
>> format, and as I learnt that the coordinates are written in .trr or
>> .xtc file and i also have a md_0_1.gro file, so can i use editconf -f
>> md_0_1.gro -o md_0_1.pdb command to convert the coordinates of the
>> simulated protein into PDB format,is it ok..
>>
>> or else should i use trjconv -f md_0_1.xtc -o md_0_1.pdb.Please
>> suggest me the correct script.
>>
>
> It depends on what you want.  If you want to use the structure from the end
> of 1 ns, use editconf.  Using trjconv to convert an .xtc file to a .pdb file
> will generate a (potentially) very large .pdb trajectory with all of the
> frames you saved.  Probably not what you want.  If there is an intermediate
> frame you want to utilize, use trjconv -dump.
>
>> Regarding docking when I did solvent simulation on GUI commercial
>> software, I used to minimize the simulated structure for docking, but
>> i have no clues learnt in gromacs tutorial ( iam new to gromacs)
>> regarding the output whether it is  minimized after simulation or not
>> the md.mdp file which i used for the production MD is as below:
>>
>
> The structure is minimized after energy minimization, which only provides a
> reasonable attempt at generating a starting structure.  Once the dynamics
> begin, the goal is to reach a equilibrium sampling of
> physiologically-relevant configurations.  The structure may or may not
> deviate substantially from the minimized structure (you can gauge that to
> some extent by RMSD).
>
> Probably the purpose of minimization before docking is simply to correct any
> weird geometry that may be present in the receptor structure
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Nicolas SAPAY]

Hi,

All TCL scripts dowloaded from the VMD website as well as mine are
supposed to be used within VMD. You have to run VMD first, then source the
script. Alternatively, you can source it in your .vmdrc file. After that,
you can run the g_cg function

Nicolas

> 
> 
> 
>   
>   
> 
> 
> HI all,
> 
> I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD
> website. But both of them can only deal with single chain system. Take
> an example, if there are 10 proteins (+water) in my system,  how to
> convert to topology of the total system to .psf file? I tried to append
> the .psf. But VMD doesn't recognize the appended .psf file.
> 
> Another question: 
> How to use the code from Nicolas? I got the following error information
> from 
>  ./coarse_grain.tcl -tpr em.tpr
> 
> : command not found line 10:
> ./coarse_grain.tcl: line 14: proc: command not found
> : command not found line 15:
> ./coarse_grain.tcl: line 17: global: command not found
> ./coarse_grain.tcl: line 18: global: command not found
> ./coarse_grain.tcl: line 19: global: command not found
> ./coarse_grain.tcl: line 20: global: command not found
> ./coarse_grain.tcl: line 21: global: command not found
> ./coarse_grain.tcl: line 22: global: command not found
> ./coarse_grain.tcl: line 23: global: command not found
> ./coarse_grain.tcl: line 24: global: command not found
> ./coarse_grain.tcl: line 25: global: command not found
> : command not found line 26:
> : command not found line 41:
> : command not found line 45:
> ./coarse_grain.tcl: line 120: syntax error near unexpected token `}'
> '/coarse_grain.tcl: line 120: ` } else {
> 
> best wishes,
> Baofu Qiao
> 
> Nicolas SAPAY wrote:
>   cite="mid:49e9485f32667c27440f5b0b836a3bf4.squir...@webmail.cermav.cnrs.fr"
>  type="cite">
>   
> Justin A. Lemkul wrote:
> 
> 
>   I have also added a Perl script to the GROMACS site
> (the VMD page):
>
>  href="http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD";>http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD
>
> The user provides an input topology file, and a .psf file is written,
> which can be loaded as data for the structure in VMD.  The !NBOND
> section seems to be the most important in this regard, so the other
> sections are a bit rough, but it seems to work alright.
>
> The caveat is the topology must be one generated by MARTINI, in order to
> satisfy all the pattern matching and the order of the topology.  It
> should be fairly easy to modify the program further to accommodate other
> layouts, but I haven't had the need to do so.
>   
> 
> I added text to the above page describing both scripts,
> which are
> attached. I'd have done that yesterday but the website was
> intermittently down.
> 
>   
>   
> Thanks for posting the tcl script on the website, although this script has
> been mainly coded by someone else. I have simply modified it for my own
> purpose.
>
> I also want to mention it is a good think to create a psf file if one work
> with VMD. You store at once, bonds, atom types and charges. Actually, I
> should have somewhere a .rtf file for the Martini amino acids and lipids
> (the equivalent of the Gromacs rtp file for CHARMM). It can be used by
> psfgen to generate a psf file with Martini bonds, charges and atom types.
> If I can retrieve it in my archives, I will post it on the website.
>
> Nicolas
>
>   
>   
> Mark
>
> 
> 
>   Nicolas Sapay wrote:
>   
>   
> Hello Thomas,
>
> I have a tcl script in my personal script library that might do what
> you want to do. I didn't use it for quite a while, but it was working
> well as far as I remember. I think it has been adapted from a script
> available on the VMD website, but I don't remember exactly its
> history. It doesn't seem too difficult to understand. You should be
> able to modify it for your own purpose, if needed.
>
> Cheers,
> Nicolas
>
>
> Thomas Schmidt a écrit :
> 
> 
>   Dear Omer,
>
> many thanks for your answer, but your solution doesn't work for me.
> We have Protein-Lipid models in the CG scale.
> Only if I replace all atom names in the PDB file through "CA" I can
> use
> the "trace" drawing method, but get also wrong atoms connected to each
> other. For example CG Beads with low distances to each other, e.g. in
> coarse-grained benzene rings, were not connected. I guess that this
> method is distance dependent, too, but in another way. :-)
>
> Does anybody else have a solution (...to put GROMACS bond information
> into VMD)?
>
> Thomas
>
>
>   
> 
> ___
> gmx-users mailing list href="mailto:gmx-users@gromacs.org";>gmx-users@gromacs.org
>  href="http://lists.gromacs.org/mailman/listinfo/gmx-users";>http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at  href="http://www.gromacs.org/search";>http://www.gromacs.org/search
> before
> posting!
> Please

Re: [gmx-users] energy minimization with position restraint

[Justin A. Lemkul]

leila karami wrote:
how can I do energy minimization with position restraint. how I creat 
cooresponding mdp file? what should considered except what is seen in 
below mdp file.




Reading the manual, wiki, and the many tutorials available will give you the 
background you need.  The obvious question comes to mind - did you try it?


-Justin


define=  -DPOSRES
constraints =  none
integrator   =  steep
nsteps   =  100
emtol=  2000
emstep =  0.01
nstcomm   =  1
ns_type =  grid
rlist   =  1
rcoulomb   =  1.0
rvdw =  1.0
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no




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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] pdb file

[Justin A. Lemkul]

leila karami wrote:
my pdb file for dna and protein contains 640 and 1130 atoms 
respectively. if I want creat a new pdb file for studying pr-dna 
interaction, should be numbering and order of numbers changed? how?




Numbering is the least of your worries, generating a reasonable starting 
structure is much more difficult, if the protein and DNA molecules are in 
separate structure files.  Once the system is assembled, it can be renumbered 
(genconf -renumber); the order is dependent only upon the order specified in the 
[molecules] directive of the topology.


-Justin





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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

[Justin A. Lemkul]

ram bio wrote:

Dear Mark,

Thanks for the advice and suggestions.

I have used trjconv command as in the justin tutorial (trjconv -s
md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact),
but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD,
i could not see the protein jumping out of the box on one side. I am
doing something wrong, Please let me know, and  was able to calculate
rmsd plot as per the command: g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc
-o rmsd.xvg -tu ns



If you don't see the protein jumping, then what's the problem?  That's the point 
of using trjconv - to correct periodicity.




and i want convert the coordinates of the simulated protein in pdb
format, and as I learnt that the coordinates are written in .trr or
.xtc file and i also have a md_0_1.gro file, so can i use editconf -f
md_0_1.gro -o md_0_1.pdb command to convert the coordinates of the
simulated protein into PDB format,is it ok..

or else should i use trjconv -f md_0_1.xtc -o md_0_1.pdb.Please
suggest me the correct script.



It depends on what you want.  If you want to use the structure from the end of 1 
ns, use editconf.  Using trjconv to convert an .xtc file to a .pdb file will 
generate a (potentially) very large .pdb trajectory with all of the frames you 
saved.  Probably not what you want.  If there is an intermediate frame you want 
to utilize, use trjconv -dump.



Regarding docking when I did solvent simulation on GUI commercial
software, I used to minimize the simulated structure for docking, but
i have no clues learnt in gromacs tutorial ( iam new to gromacs)
regarding the output whether it is  minimized after simulation or not
the md.mdp file which i used for the production MD is as below:



The structure is minimized after energy minimization, which only provides a 
reasonable attempt at generating a starting structure.  Once the dynamics begin, 
the goal is to reach a equilibrium sampling of physiologically-relevant 
configurations.  The structure may or may not deviate substantially from the 
minimized structure (you can gauge that to some extent by RMSD).


Probably the purpose of minimization before docking is simply to correct any 
weird geometry that may be present in the receptor structure


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] energy minimization with position restraint

[Kukol, Andreas]

Apart from specifying -DPOSRES in your mdp file, you need to make sure that 
posre.itp will be included into your topology. There is usually a statement 
like 'ifdef POSRES ..."

Andreas

---

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of leila karami
Sent: 21 October 2009 13:24
To: gmx-users@gromacs.org
Subject: [gmx-users] energy minimization with position restraint

how can I do energy minimization with position restraint. how I creat 
cooresponding mdp file? what should considered except what is seen in below mdp 
file.

define=  -DPOSRES
constraints =  none
integrator   =  steep
nsteps   =  100
emtol=  2000
emstep =  0.01
nstcomm   =  1
ns_type =  grid
rlist   =  1
rcoulomb   =  1.0
rvdw =  1.0
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no
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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Justin A. Lemkul]

Baofu Qiao wrote:

HI all,

I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD 
website. But both of them can only deal with single chain system. Take 
an example, if there are 10 proteins (+water) in my system,  how to 
convert to topology of the total system to .psf file? I tried to append 
the .psf. But VMD doesn't recognize the appended .psf file.




I can't comment on Nicolas' script, but as for my own, you need to supply a 
single topology, there is no way to append the output.  You could, for 
visualization purposes, separate the coordinates of each of your subunits from 
the assembled structure, generate the corresponding .psf file for each, and load 
them all separately into VMD.  A little tedious, I know, but given the method 
for generating MARTINI topologies, I'm not sure I can provide a better method.


-Justin


Another question:
How to use the code from Nicolas? I got the following error information 
from

  ./coarse_grain.tcl -tpr em.tpr

: command not found line 10:
./coarse_grain.tcl: line 14: proc: command not found
: command not found line 15:
./coarse_grain.tcl: line 17: global: command not found
./coarse_grain.tcl: line 18: global: command not found
./coarse_grain.tcl: line 19: global: command not found
./coarse_grain.tcl: line 20: global: command not found
./coarse_grain.tcl: line 21: global: command not found
./coarse_grain.tcl: line 22: global: command not found
./coarse_grain.tcl: line 23: global: command not found
./coarse_grain.tcl: line 24: global: command not found
./coarse_grain.tcl: line 25: global: command not found
: command not found line 26:
: command not found line 41:
: command not found line 45:
./coarse_grain.tcl: line 120: syntax error near unexpected token `}'
'/coarse_grain.tcl: line 120: ` } else {

best wishes,
Baofu Qiao

Nicolas SAPAY wrote:

Justin A. Lemkul wrote:


I have also added a Perl script to the GROMACS site (the VMD page):

http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD

The user provides an input topology file, and a .psf file is written,
which can be loaded as data for the structure in VMD.  The !NBOND
section seems to be the most important in this regard, so the other
sections are a bit rough, but it seems to work alright.

The caveat is the topology must be one generated by MARTINI, in order to
satisfy all the pattern matching and the order of the topology.  It
should be fairly easy to modify the program further to accommodate other
layouts, but I haven't had the need to do so.
  

I added text to the above page describing both scripts, which are
attached. I'd have done that yesterday but the website was
intermittently down.



Thanks for posting the tcl script on the website, although this script has
been mainly coded by someone else. I have simply modified it for my own
purpose.

I also want to mention it is a good think to create a psf file if one work
with VMD. You store at once, bonds, atom types and charges. Actually, I
should have somewhere a .rtf file for the Martini amino acids and lipids
(the equivalent of the Gromacs rtp file for CHARMM). It can be used by
psfgen to generate a psf file with Martini bonds, charges and atom types.
If I can retrieve it in my archives, I will post it on the website.

Nicolas

  

Mark



Nicolas Sapay wrote:
  

Hello Thomas,

I have a tcl script in my personal script library that might do what
you want to do. I didn't use it for quite a while, but it was working
well as far as I remember. I think it has been adapted from a script
available on the VMD website, but I don't remember exactly its
history. It doesn't seem too difficult to understand. You should be
able to modify it for your own purpose, if needed.

Cheers,
Nicolas


Thomas Schmidt a écrit :


Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can
use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas


  

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[gmx-users] energy minimization with position restraint

[leila karami]

how can I do energy minimization with position restraint. how I creat
cooresponding mdp file? what should considered except what is seen in below
mdp file.

define=  -DPOSRES
constraints =  none
integrator   =  steep
nsteps   =  100
emtol=  2000
emstep =  0.01
nstcomm   =  1
ns_type =  grid
rlist   =  1
rcoulomb   =  1.0
rvdw =  1.0
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no
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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Baofu Qiao]

HI all,

I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD
website. But both of them can only deal with single chain system. Take
an example, if there are 10 proteins (+water) in my system,  how to
convert to topology of the total system to .psf file? I tried to append
the .psf. But VMD doesn't recognize the appended .psf file.

Another question: 
How to use the code from Nicolas? I got the following error information
from 
 ./coarse_grain.tcl -tpr em.tpr

: command not found line 10:
./coarse_grain.tcl: line 14: proc: command not found
: command not found line 15:
./coarse_grain.tcl: line 17: global: command not found
./coarse_grain.tcl: line 18: global: command not found
./coarse_grain.tcl: line 19: global: command not found
./coarse_grain.tcl: line 20: global: command not found
./coarse_grain.tcl: line 21: global: command not found
./coarse_grain.tcl: line 22: global: command not found
./coarse_grain.tcl: line 23: global: command not found
./coarse_grain.tcl: line 24: global: command not found
./coarse_grain.tcl: line 25: global: command not found
: command not found line 26:
: command not found line 41:
: command not found line 45:
./coarse_grain.tcl: line 120: syntax error near unexpected token `}'
'/coarse_grain.tcl: line 120: ` } else {

best wishes,
Baofu Qiao

Nicolas SAPAY wrote:

  
Justin A. Lemkul wrote:


  I have also added a Perl script to the GROMACS site (the VMD page):

http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD

The user provides an input topology file, and a .psf file is written,
which can be loaded as data for the structure in VMD.  The !NBOND
section seems to be the most important in this regard, so the other
sections are a bit rough, but it seems to work alright.

The caveat is the topology must be one generated by MARTINI, in order to
satisfy all the pattern matching and the order of the topology.  It
should be fairly easy to modify the program further to accommodate other
layouts, but I haven't had the need to do so.
  

I added text to the above page describing both scripts, which are
attached. I'd have done that yesterday but the website was
intermittently down.

  
  
Thanks for posting the tcl script on the website, although this script has
been mainly coded by someone else. I have simply modified it for my own
purpose.

I also want to mention it is a good think to create a psf file if one work
with VMD. You store at once, bonds, atom types and charges. Actually, I
should have somewhere a .rtf file for the Martini amino acids and lipids
(the equivalent of the Gromacs rtp file for CHARMM). It can be used by
psfgen to generate a psf file with Martini bonds, charges and atom types.
If I can retrieve it in my archives, I will post it on the website.

Nicolas

  
  
Mark



  Nicolas Sapay wrote:
  
  
Hello Thomas,

I have a tcl script in my personal script library that might do what
you want to do. I didn't use it for quite a while, but it was working
well as far as I remember. I think it has been adapted from a script
available on the VMD website, but I don't remember exactly its
history. It doesn't seem too difficult to understand. You should be
able to modify it for your own purpose, if needed.

Cheers,
Nicolas


Thomas Schmidt a écrit :


  Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can
use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas


  

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[gmx-users] pdb file

[leila karami]

my pdb file for dna and protein contains 640 and 1130 atoms respectively. if
I want creat a new pdb file for studying pr-dna interaction, should be
numbering and order of numbers changed? how?
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Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

[ram bio]

Dear Mark,

Thanks for the advice and suggestions.

I have used trjconv command as in the justin tutorial (trjconv -s
md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact),
but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD,
i could not see the protein jumping out of the box on one side. I am
doing something wrong, Please let me know, and  was able to calculate
rmsd plot as per the command: g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc
-o rmsd.xvg -tu ns


and i want convert the coordinates of the simulated protein in pdb
format, and as I learnt that the coordinates are written in .trr or
.xtc file and i also have a md_0_1.gro file, so can i use editconf -f
md_0_1.gro -o md_0_1.pdb command to convert the coordinates of the
simulated protein into PDB format,is it ok..

or else should i use trjconv -f md_0_1.xtc -o md_0_1.pdb.Please
suggest me the correct script.

Regarding docking when I did solvent simulation on GUI commercial
software, I used to minimize the simulated structure for docking, but
i have no clues learnt in gromacs tutorial ( iam new to gromacs)
regarding the output whether it is  minimized after simulation or not
the md.mdp file which i used for the production MD is as below:

title   = MD
integrator  = md
nsteps  = 50
dt  = 0.002 
nstxout = 1000  
nstvout = 1000  
nstxtcout   = 1000  
nstenergy   = 1000  
nstlog  = 1000  
continuation= yes   
constraint_algorithm = lincs
constraints = all-bonds 
lincs_iter  = 1 
lincs_order = 4 
ns_type = grid  
nstlist = 5 
rlist   = 1.0   
rcoulomb= 1.0   
rvdw= 1.0   
coulombtype = PME   
pme_order   = 4 
fourierspacing  = 0.16  
; Temperature coupling is on
tcoupl  = V-rescale 
tc-grps = Protein Non-Protein   
tau_t   = 0.1   0.1 
ref_t   = 300   300 
pcoupl  = Parrinello-Rahman 
pcoupltype  = isotropic 
tau_p   = 2.0   
ref_p   = 1.0   
compressibility = 4.5e-5
pbc = xyz   
DispCorr= EnerPres  
gen_vel = no

Thanks,

Ram 



On Wed, Oct 21, 2009 at 4:42 PM, Mark Abraham  wrote:
> ram bio wrote:
>>
>> Dear Gromacs Users,
>>
>> I have performed a protein in solvent simulation for 1 ns, the got the
>> output files as: md_0_1.cpt  md_0_1.edr  md_0_1.gro  md_0_1.log
>> md_0_1.tpr  md_0_1.trr  md_0_1.xtc. I am following Justin Tutorial.
>>
>> Can anybody tell me how to extract the coordinates ? of the simulated
>> protein (file after extraction ?) and is it necessary to minimize the
>
> It sounds like you should be doing more tutorials to understand GROMACS
> workflows better. What coordinates you produced are in the .trr or .xtc
> files, but what data is there with what frequency is set up in your .mdp
> file, so you need to plan that in advance. trjconv is the tool for
> manipulating those files, for example to extract frames as PDB to use with
> some other software.
>
>> simulated protein in vacco to use it for further docking studies.
>
> Maybe. Read the docking literature, or do some tutorials there.
>
> Mark
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Re: [gmx-users] how to mimick explicit hydrogen bonding

[ms]

Hi Mark,

Thanks for your answer.

Mark Abraham ha scritto:
> There's nothing directional about the physics of a hydrogen bond, unless
> your model makes it so. There'd be nothing intrinsically valid or
> invalid with that either, so long as you parameterized the force field
> under that assumption. If using rigid water models and/or other atomic
> constraints where H-bonded atoms can't have a geometric distortion, I
> suppose such a model might be necessary. It's still far from clear that
> H-bonding is sufficiently different from other electrostatic
> interactions to warrant special treatment (and thus reparameterization
> of charges).

Ok, the problem is that I want to re-implement a quite minimal
coarse-grained FF (so no explicit solvent etc.) and a directional
interaction would be useful.

>> Can anyone give me hints on how to describe a directional
>> hydrogen-bond-like interaction?
> 
> You would not achieve this in GROMACS without code modification. A
> special non-bonded list for H-bonded water (and maybe H-bonded
> non-water) that didn't call the standard water inner loops would be
> required.

I see. I asked because I think I've read that there were force fields
with explicit hydrogen bond treatment (some CHARMM?) that were imported
into Gromacs, and I thought there was some clever hack to get it working
-but I guess that it is not the case.

Thanks!
m.
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Re: [gmx-users] mdp file

[Mark Abraham]

leila karami wrote:

dear Mark

thanks for your attention. is this mdp file true for energy minimization 
(100 steps by steepest descent and 100 steps by/ conjugate gradient/)?


define=  -DFLEX_SPC
constraints =  none
*integrator  =  steep
nsteps   =  100
integrator  =  cg
nsteps   =  100*
emtol =  2000
emstep  =  0.01
nstcomm   =  1
ns_type =  grid
rlist   =  1
rcoulomb   =  1.0
rvdw =  1.0
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no


No - you should have tried it to see what you got. grompp probably gives 
an error because you cannot define integrator twice. You need to have 
two mdp files and do a pair of (grompp - mdrun) operations.


Mark
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Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

[Mark Abraham]

ram bio wrote:

Dear Gromacs Users,

I have performed a protein in solvent simulation for 1 ns, the got the
output files as: md_0_1.cpt  md_0_1.edr  md_0_1.gro  md_0_1.log
md_0_1.tpr  md_0_1.trr  md_0_1.xtc. I am following Justin Tutorial.

Can anybody tell me how to extract the coordinates ? of the simulated
protein (file after extraction ?) and is it necessary to minimize the


It sounds like you should be doing more tutorials to understand GROMACS 
workflows better. What coordinates you produced are in the .trr or .xtc 
files, but what data is there with what frequency is set up in your .mdp 
file, so you need to plan that in advance. trjconv is the tool for 
manipulating those files, for example to extract frames as PDB to use 
with some other software.



simulated protein in vacco to use it for further docking studies.


Maybe. Read the docking literature, or do some tutorials there.

Mark
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[gmx-users] mdp file

[leila karami]

dear Mark

thanks for your attention. is this mdp file true for energy minimization
(100 steps by steepest descent and 100 steps by* conjugate gradient*)?

define=  -DFLEX_SPC
constraints =  none
*integrator  =  steep
nsteps   =  100
integrator  =  cg
nsteps   =  100*
emtol =  2000
emstep  =  0.01
nstcomm   =  1
ns_type =  grid
rlist   =  1
rcoulomb   =  1.0
rvdw =  1.0
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no
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Re: [gmx-users] gmx-users:Running gromacs on IBM cluster

[Mark Abraham]

Nkwe Monama wrote:

Dear gmx-users,

I have been trying to run gromacs on IBM cluster on multiple nodes using 
loadleveler script.
Do I have to compile gromacs on individual nodes? What do I have to do to run 
it on multiple nodes?


That will depend how what your cluster is and how it is set up to work. 
It's more a question for your system admins, since it is not 
GROMACS-specific.



I get the following error message:

llsetpenv: execve failed with rc=-1 and errno=2
10/21 09:03:56 TI-0 chpcln.221953.0 Sending startup failure message to parent 
Starter.


That's a generic failure message from Loadleveler.

Mark
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[gmx-users] Protein Solvent Dynamics - Coordinates for docking

[ram bio]

Dear Gromacs Users,

I have performed a protein in solvent simulation for 1 ns, the got the
output files as: md_0_1.cpt  md_0_1.edr  md_0_1.gro  md_0_1.log
md_0_1.tpr  md_0_1.trr  md_0_1.xtc. I am following Justin Tutorial.

Can anybody tell me how to extract the coordinates ? of the simulated
protein (file after extraction ?) and is it necessary to minimize the
simulated protein in vacco to use it for further docking studies.

Please help.

Thanks,

ram
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Re: [gmx-users] Box vector error

[Mark Abraham]

I tried to restart simulation, going back,  from the time point where there was
no substantial change in the dimensions of the box, but simulations aborts again
after some time with the same error. The time points at which simulation aborts
are random. Having simulated for 25ns now i do not want to change the box shape
and resimulate everything again.


So there's a good lesson for all computational chemists: check your 
output is well-formed before you invest computer time heavily in a method.


Mark
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Re: [gmx-users] mdp file

[Mark Abraham]

leila karami wrote:

Hi
I want to creat mdp file for energy minimization (em.mdp). if I want to 
minimize my system (pr+dna), by steepest descent and conjugate gradient 
such as for example 100 steps by steepest descent and 100 steps by 
conjugate gradient, how I can  creat  mdp file?


For example, take one from a tutorial, consider whether each parameter 
is suitable for your needs, change as suitable, use.


Mark
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[gmx-users] pdb file

[leila karami]

my pdb file for dna and protein contains 640 and 1130 atoms respectively. if
I want creat a new pdb file for studying pr-dna interaction, should be
numbering and order of numbers changed? how?
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[gmx-users] mdp file

[leila karami]

Hi
I want to creat mdp file for energy minimization (em.mdp). if I want to
minimize my system (pr+dna), by steepest descent and conjugate gradient such
as for example 100 steps by steepest descent and 100 steps by conjugate
gradient, how I can  creat  mdp file?
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[gmx-users] Re: CMAP request

[Sudip Roy]

Hi Paer,

  Thank you very much for your mail.
Here is the paper from where we are taking the MTSSL parameters

J. Phys. Chem. B 2008 112, 5755-5767, by B. Roux
and the supplementary in it.

Thank you.

Sudip



Pär Bjelkmar wrote:

Hi,

21 okt 2009 kl. 10.59 skrev Sudip Roy:

 Thank you very much for your reply.
MTSSL is not a peptide, but it was parameterized by some
other group and we are trying to use the parameters. They have
used CMAP for MTSSL. So we also want to
take into account the CMAP in our gromacs calculations.


This is very strange! You are sure the molecule works in CHARMM? I 
mean there's only three CMAPs parameterized in the CHARMM force field; 
ALA, PRO and GLY and MTSSL does not contain any amino acids so I guess 
must have parameterized new CMAPs then. I would very much like to see 
the CHARMM definition of this molecule if you don't mind.



I am not much familiar with git repo. It  will be very kind of you
if you send us a copy of gromacs 4.1 and CHARMM27 ff file
with CMAP in gromacs format, so that we can include this
ff also in our database.
Well, follow the instructions here: 
http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage
and compile the source (instructions on the webpage also) on your 
platform.


Then place the ffcharmm27 files in the attachment in the current 
working directory (or place them in the share/top/ directory of the 
installation).


Regards,
Pär Bjelkmar





--
**

Dr. Sudip Roy
Physical Chemistry and Material Science Division
Scientist C
National Chemical Laboratory
Pune 411008
India 


Tel.  +91 2590 2735 Office
Email s@ncl.res.in


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Re: [gmx-users] Re: how to calculate g_sdf and ionic conductivity

[Tsjerk Wassenaar]

 with a coordinate file for one molecule, use genconf to generate a box, and
> equilibrate.
>
> If you want any further information about diagnosing the current problem,
> posting the .mdp file would be helpful.
>
> -Justin
>
>>
>> Thanks again!
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
> --
>
> Message: 2
> Date: Wed, 21 Oct 2009 10:18:19 +0800
> From: "Jinyao Wang" 
> Subject: [gmx-users] why are the values of the LJ interaction energy
> negative and the values of the Coulomb interaction energypositive
> between two group.
> To: "gmx-users" 
> Message-ID: <456090806.02...@ciac.jl.cn>
> Content-Type: text/plain;charset="gb2312"
>
> Hi gmx-users,
>   I have calculated the interaction energy between two group. But I find
> that the values of the LJ interaction energy are negative and the values of
> the Coulomb interaction energy are positive between two group. So I think
> the LJ interaction is attractive and the Coulomb interaction is repulsive.
> Is it correct for my consideration of the interaction ?
>
>
>
>
>
> Jinyao Wang
> wan...@ciac.jl.cn
> 　　2009-10-21
>
> --
>
> Message: 3
> Date: Wed, 21 Oct 2009 13:26:22 +1100
> From: Mark Abraham 
> Subject: Re: [gmx-users] why are the values of the LJ interaction
> energynegativeand the values of the Coulomb interaction energy
> positive between twogroup.
> To: Discussion list for GROMACS users 
> Message-ID: <4ade714e.5000...@anu.edu.au>
> Content-Type: text/plain; charset=GB2312
>
> Jinyao Wang wrote:
>> Hi gmx-users,
>>I have calculated the interaction energy between two group. But I find
>> that the values of the LJ interaction energy are negative and the values of
>> the Coulomb interaction energy are positive between two group. So I think
>> the LJ interaction is attractive and the Coulomb interaction is repulsive.
>> Is it correct for my consideration of the interaction ?
>
> Maybe. That conclusion would assume
> a) that you've calculated it correctly,
> b) that the model physics is robust with respect to such a decomposition
> when it almost certainly wasn't parameterized for such a property, and
> c) the decomposed interaction energy means anything.
>
> Mark
>
>
> --
>
> Message: 4
> Date: Wed, 21 Oct 2009 10:31:49 +0800
> From: wuxiao 
> Subject: [gmx-users] Fatal error: 2 particles communicated to PME node
> 0 are more than a cell length out of the domain decomposition cell of
> their charge group
> To: 
> Message-ID: 
> Content-Type: text/plain; charset="gb2312"
>
>
> Dear GMXers,
>
>   When I perfomed a MD simulation, it always teminated after about 700 ps
> with the message:
>
> Fatal error: 2 particles communicated to PME node 0 are more than a cell
> length out of the domain decomposition cell of their charge group
>
>   I utilized the GROMACS-4.0.5. I have searched the maillist to find some
> similar posts but they can not yet cope with this issues. Could you give me
> some clues, please?
>
>   Best wishes,
>
>   Chaofu Wu, Dr.
>
> _
> Messenger安全保护中心，免费修复系统漏洞，保护Messenger安全！
> http://im.live.cn/safe/
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20091021/c8985b2e/attachment-0001.html
>
> --
>
> Message: 5
> Date: Wed, 21 Oct 2009 13:58:24 +1100
> From: Mark Abraham 
> Subject: Re: [gmx-users] Fatal error: 2 particles communicated to PME
> node0 are more than a cell length out of the domain decomposition
> cell oftheir charge group
> To: Discussion list for GROMACS users 
&g

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Nicolas SAPAY]

> Justin A. Lemkul wrote:
>>
>> I have also added a Perl script to the GROMACS site (the VMD page):
>>
>> http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD
>>
>> The user provides an input topology file, and a .psf file is written,
>> which can be loaded as data for the structure in VMD.  The !NBOND
>> section seems to be the most important in this regard, so the other
>> sections are a bit rough, but it seems to work alright.
>>
>> The caveat is the topology must be one generated by MARTINI, in order to
>> satisfy all the pattern matching and the order of the topology.  It
>> should be fairly easy to modify the program further to accommodate other
>> layouts, but I haven't had the need to do so.
>
> I added text to the above page describing both scripts, which are
> attached. I'd have done that yesterday but the website was
> intermittently down.

Thanks for posting the tcl script on the website, although this script has
been mainly coded by someone else. I have simply modified it for my own
purpose.

I also want to mention it is a good think to create a psf file if one work
with VMD. You store at once, bonds, atom types and charges. Actually, I
should have somewhere a .rtf file for the Martini amino acids and lipids
(the equivalent of the Gromacs rtp file for CHARMM). It can be used by
psfgen to generate a psf file with Martini bonds, charges and atom types.
If I can retrieve it in my archives, I will post it on the website.

Nicolas

>
> Mark
>
>> Nicolas Sapay wrote:
>>> Hello Thomas,
>>>
>>> I have a tcl script in my personal script library that might do what
>>> you want to do. I didn't use it for quite a while, but it was working
>>> well as far as I remember. I think it has been adapted from a script
>>> available on the VMD website, but I don't remember exactly its
>>> history. It doesn't seem too difficult to understand. You should be
>>> able to modify it for your own purpose, if needed.
>>>
>>> Cheers,
>>> Nicolas
>>>
>>>
>>> Thomas Schmidt a écrit :
 Dear Omer,

 many thanks for your answer, but your solution doesn't work for me.
 We have Protein-Lipid models in the CG scale.
 Only if I replace all atom names in the PDB file through "CA" I can
 use
 the "trace" drawing method, but get also wrong atoms connected to each
 other. For example CG Beads with low distances to each other, e.g. in
 coarse-grained benzene rings, were not connected. I guess that this
 method is distance dependent, too, but in another way. :-)

 Does anybody else have a solution (...to put GROMACS bond information
 into VMD)?

 Thomas


>>>
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
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>>
> ___
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>


-- 
[ Nicolas Sapay - Post-Doctoral Fellow ]
CERMAV - www.cermav.cnrs.fr
BP53, 38041 Grenoble cedex 9, France
Phone: +33 (0)4 76 03 76 44/53

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RE: [gmx-users] g_rdf and number of atoms to include

[Enemark Soeren]

Hi Omer,

Thanks for your input.

 

Let me reformulate my problem:

 

I have glycine molecules in the form of zwitterions:

 

 

1ZGLY N1   0.560   0.337   0.388 -0.0759 -0.2488 -0.5471

1ZGLYH12   0.625   0.312   0.461  0.6035  0.5922 -0.4315

1ZGLYH23   0.601   0.311   0.299  0.1500 -0.3357 -1.5372

1ZGLYH34   0.553   0.433   0.388  0.5086  2.8817 -1.8023

1ZGLYCA5   0.426   0.272   0.403  0.3095  0.1790 -0.0455

1ZGLY   HA16   0.352   0.335   0.345 -0.9032  0.4782  0.1366

1ZGLY   HA27   0.433   0.173   0.358  0.7875  0.5369 -3.0389

1ZGLY C8   0.378   0.267   0.551  0.1816 -0.4672  0.1868

1ZGLY   OC19   0.449   0.218   0.644 -0.2820 -0.4080  0.2048

1ZGLY   OC2   10   0.263   0.320   0.559 -0.0662 -0.2935 -0.8010

 

 

Now, I am interested in the interaction between the amine group hydrogen
atoms (H1, H2, and H3) and the water oxygen atom. Thus, I define 2 group
in an index file:

1.   aH1H2H3 (which contains all H1, H2, and H3 atoms in the glycine
molecules in my system)

2.   aOwat (which contains all oxygen atoms in the water molecules
in my system)

 

However, I also tried setting up a different index file with the groups:

1.   aH1 (which contains all H1 atoms in my system)

2.   aOwat (like before)

 

I find that these 2 index files do not produce the same RDFs. Why is
that?

 

 

Best regards,

Soren

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Omer Markovitch
Sent: Wednesday, October 21, 2009 4:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_rdf and number of atoms to include

 

On Wed, Oct 21, 2009 at 07:28, Enemark Soeren  wrote:

Dear users,

I would like to compare interactions between molecules by using RDF. I
have tried looking at glycine and water, and compare the following two
interactions:

1)  between the amine hydrogen atoms in glycine and the oxygen atom
in water

2)  between the carboxyl oxygen atoms in glycine and the oxygen atom
in water 

However, my result in 1) depends on how many of the 3 hydrogen atoms I
include in the calculations. Why is that?

If you mean that when focusing your RDF calculations on either one of
the three hydrogens results in three different RDFs then it means that
each hydrogen feels water differently. I bet this difference is only for
the first peak of g(r) and the other peaks overlap between the three
RDFs. As for how reasonable this result, its not unlikely because
glycine has atleast 2 different types of hydrogens (say, C-H vs. N-H),
depending on the protonation state. You might want to provide more
details on the system you are studying to get better answer.
I am assuming that the RDFs are converged so that including more
trajectory data and/or sampled molecules and/or changing bin size does
not result in a drastic change to the curves.



 

Does that mean that I cannot directly compare the strengths (RDF
peak height) of the two interactions as they are not based on the same
number of atoms? Does it also mean that I must always calculate RDFs by
using 1 atom on each of the particles/groups that I am comparing?

I am not sure how good it is to use the first peak of g(r) to analyze
strengths, but you should also consider the width and area under peak.
This peak is an average on all nearest neighbours, bonded or not, so it
might not give you a good estimate of the hydrogen bond, for example.
If you are unsure of your g(r) calc it just for water (that is - only
oxygen-oxygen of water-water). At long distances (~10 Angstroms) it
should fluctuate around 1.

Bests, Omer Markovitch. 

 

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Re: [gmx-users] Box vector error

[Tsjerk Wassenaar]

Hi Prem,

There is just something terribly wrong with your system if it goes
flat like that. But with only the information you give here, no one
can tell you more than that.

Cheers,

Tsjerk

On Wed, Oct 21, 2009 at 10:18 AM, Prem Singh Kaushal
 wrote:
> Dear All
>
>     I am using GROMCS 3.3.1 version. I had started the simulation of protein 
> in
> water with an octahedral box of dimension 9.76276   9.20449   7.97128   
> 0.0
>  0.0   3.25425   0.0  -3.25425  4.60225. However after 25ns the
> simulation aborts with the following error:
>
> Fatal error:
> One of the box vectors has become shorter than twice the cut-off length or one
> of the box diagonal elements has become smaller than the cut-off.
> The box size at this pint is
>
> At this time point box has changed drastically with vectors,   2.61137  
> 15.10480
>  18.99570   0.0   0.0   0.2   0.0   0.2   0.3.
>
> I tried to restart simulation, going back,  from the time point where there 
> was
> no substantial change in the dimensions of the box, but simulations aborts 
> again
> after some time with the same error. The time points at which simulation 
> aborts
> are random. Having simulated for 25ns now i do not want to change the box 
> shape
> and resimulate everything again.
>
> I shall appreciate you prompt suggestions regarding this.
>
> With regards
> Prem
>
>
>
>
>
> --
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-- 
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Junior UD (post-doc)
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Utrecht University
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[gmx-users] Re: how to calculate g_sdf and ionic conductivity

[naimah haron naimah]

A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




--

Message: 2
Date: Wed, 21 Oct 2009 10:18:19 +0800
From: "Jinyao Wang" 
Subject: [gmx-users] why are the values of the LJ interaction energy
negative and the values of the Coulomb interaction energypositive
between two group.
To: "gmx-users" 
Message-ID: <456090806.02...@ciac.jl.cn>
Content-Type: text/plain;charset="gb2312"

Hi gmx-users,
   I have calculated the interaction energy between two group. But I find that 
the values of the LJ interaction energy are negative and the values of the 
Coulomb interaction energy are positive between two group. So I think the LJ 
interaction is attractive and the Coulomb interaction is repulsive. Is it 
correct for my consideration of the interaction ?  





Jinyao Wang
wan...@ciac.jl.cn
　　2009-10-21

--

Message: 3
Date: Wed, 21 Oct 2009 13:26:22 +1100
From: Mark Abraham 
Subject: Re: [gmx-users] why are the values of the LJ interaction
energynegativeand the values of the Coulomb interaction energy
positive between twogroup.
To: Discussion list for GROMACS users 
Message-ID: <4ade714e.5000...@anu.edu.au>
Content-Type: text/plain; charset=GB2312

Jinyao Wang wrote:
> Hi gmx-users,
>I have calculated the interaction energy between two group. But I find 
> that the values of the LJ interaction energy are negative and the values of 
> the Coulomb interaction energy are positive between two group. So I think the 
> LJ interaction is attractive and the Coulomb interaction is repulsive. Is it 
> correct for my consideration of the interaction ?  

Maybe. That conclusion would assume
a) that you've calculated it correctly,
b) that the model physics is robust with respect to such a decomposition
when it almost certainly wasn't parameterized for such a property, and
c) the decomposed interaction energy means anything.

Mark


--

Message: 4
Date: Wed, 21 Oct 2009 10:31:49 +0800
From: wuxiao 
Subject: [gmx-users] Fatal error: 2 particles communicated to PME node
0 are more than a cell length out of the domain decomposition cell of
their charge group
To: 
Message-ID: 
Content-Type: text/plain; charset="gb2312"


Dear GMXers,

   When I perfomed a MD simulation, it always teminated after about 700 ps with 
the message:

Fatal error: 2 particles communicated to PME node 0 are more than a cell length 
out of the domain decomposition cell of their charge group

   I utilized the GROMACS-4.0.5. I have searched the maillist to find some 
similar posts but they can not yet cope with this issues. Could you give me 
some clues, please?

  Best wishes,

  Chaofu Wu, Dr.
  
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Message: 5
Date: Wed, 21 Oct 2009 13:58:24 +1100
From: Mark Abraham 
Subject: Re: [gmx-users] Fatal error: 2 particles communicated to PME
node0 are more than a cell length out of the domain decomposition
cell oftheir charge group
To: Discussion list for GROMACS users 
Message-ID: <4ade78d0.2000...@anu.edu.au>
Content-Type: text/plain; charset=GB2312

wuxiao wrote:
> Dear GMXers,
>When I perfomed a MD simulation, it always teminated after about 700 
> ps with the message:
> /Fatal error: 2 particles communicated to PME node 0 are more than a 
> cell length out of the domain decomposition cell of their charge group/
>I utilized the GROMACS-4.0.5. I have searched the maillist to find 
> some similar posts but they can not yet cope with this issues. Could you 
> give me some clues, please?

Yep. http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Mark


--

Message: 6
Date: Wed, 21 Oct 2009 13:28:39 +0800
From: "Enemark Soeren" 
Subject: [gmx-users] g_rdf and number of atoms to include
To: "Discussion list for GROMACS users" 
Message-ID:

Content-Type: text/plain; charset="us-ascii"

Dear users,



I would like to compare interactions between molecules by using RDF. I
have tried looking at glycine and water, and compare the following two
interactions:

1)  between the amine hydrogen atoms in glycine and the oxygen atom
in water

2)  between the carboxyl oxygen atoms in glycine and the oxygen atom
in water



However, my result in 1) depends on how many of the 3 hy

[gmx-users] CMAP request

[Sudip Roy]

Dear Paer,
  Thank you very much for your reply.
MTSSL is not a peptide, but it was parameterized by some
other group and we are trying to use the parameters. They have
used CMAP for MTSSL. So we also want to
take into account the CMAP in our gromacs calculations.

I am not much familiar with git repo. It  will be very kind of you
if you send us a copy of gromacs 4.1 and CHARMM27 ff file
with CMAP in gromacs format, so that we can include this
ff also in our database.

Thanking you.

Sudip

--
**

Dr. Sudip Roy
Physical Chemistry and Material Science Division
Scientist C
National Chemical Laboratory
Pune 411008
India 


Tel.  +91 2590 2735 Office
Email s@ncl.res.in


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[gmx-users] Box vector error

[Prem Singh Kaushal]

Dear All

 I am using GROMCS 3.3.1 version. I had started the simulation of protein in
water with an octahedral box of dimension 9.76276   9.20449   7.97128   0.0 
 0.0   3.25425   0.0  -3.25425  4.60225. However after 25ns the
simulation aborts with the following error:

Fatal error:
One of the box vectors has become shorter than twice the cut-off length or one
of the box diagonal elements has become smaller than the cut-off.
The box size at this pint is

At this time point box has changed drastically with vectors,   2.61137  15.10480
 18.99570   0.0   0.0   0.2   0.0   0.2   0.3.

I tried to restart simulation, going back,  from the time point where there was
no substantial change in the dimensions of the box, but simulations aborts again
after some time with the same error. The time points at which simulation aborts
are random. Having simulated for 25ns now i do not want to change the box shape
and resimulate everything again.

I shall appreciate you prompt suggestions regarding this.

With regards
Prem





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Re: [gmx-users] g_rdf and number of atoms to include

[Omer Markovitch]

On Wed, Oct 21, 2009 at 07:28, Enemark Soeren  wrote:

>  Dear users,
>
> I would like to compare interactions between molecules by using RDF. I have
> tried looking at glycine and water, and compare the following two
> interactions:
>
> 1)  between the amine hydrogen atoms in glycine and the oxygen atom in
> water
>
> 2)  between the carboxyl oxygen atoms in glycine and the oxygen atom
> in water
>
> However, my result in 1) depends on how many of the 3 hydrogen atoms I
> include in the calculations. Why is that?
>
If you mean that when focusing your RDF calculations on either one of the
three hydrogens results in three different RDFs then it means that each
hydrogen feels water differently. I bet this difference is only for the
first peak of g(r) and the other peaks overlap between the three RDFs. As
for how reasonable this result, its not unlikely because glycine has atleast
2 different types of hydrogens (say, C-H vs. N-H), depending on the
protonation state. You might want to provide more details on the system you
are studying to get better answer.
I am assuming that the RDFs are converged so that including more trajectory
data and/or sampled molecules and/or changing bin size does not result in a
drastic change to the curves.


> Does that mean that I cannot directly compare the strengths (RDF peak
> height) of the two interactions as they are not based on the same number of
> atoms? Does it also mean that I must always calculate RDFs by using 1 atom
> on each of the particles/groups that I am comparing?
>
I am not sure how good it is to use the first peak of g(r) to analyze
strengths, but you should also consider the width and area under peak. This
peak is an average on all nearest neighbours, bonded or not, so it might not
give you a good estimate of the hydrogen bond, for example.
If you are unsure of your g(r) calc it just for water (that is - only
oxygen-oxygen of water-water). At long distances (~10 Angstroms) it should
fluctuate around 1.

Bests, Omer Markovitch.
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[gmx-users] gmx-users:Running gromacs on IBM cluster

[Nkwe Monama]

Dear gmx-users,

I have been trying to run gromacs on IBM cluster on multiple nodes using 
loadleveler script.
Do I have to compile gromacs on individual nodes? What do I have to do to run 
it on multiple nodes?

I get the following error message:

llsetpenv: execve failed with rc=-1 and errno=2
10/21 09:03:56 TI-0 chpcln.221953.0 Sending startup failure message to parent 
Starter.

Regards,
Nkwe

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Re: [gmx-users] how to calculate g_sdf and ionic conductivity

[Mark Abraham]

naimah haron naimah wrote:

Hello all

Did anyone know how to
1) calculate g_sdf?


Start with g_sdf -h.


2) ionic conductivity?


Don't know. Look in manual 7.4, 8 and maybe Appendix D.


Can I have the commands for that


If you do some more of your own work and ask focussed questions you help 
yourself look worth helping :-)


Mark
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